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- PDB-5tv5: BioW from Aquifex aeoulicus -

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Basic information

Entry
Database: PDB / ID: 5tv5
TitleBioW from Aquifex aeoulicus
Components6-carboxyhexanoate--CoA ligase
KeywordsLIGASE / Pimeloyl-CoA Ligase / adenylation
Function / homology6-carboxyhexanoate-CoA ligase / 6-carboxyhexanoate-CoA ligase activity / 6-carboxyhexanoate--CoA ligase / 6-carboxyhexanoate--CoA ligase / biotin biosynthetic process / magnesium ion binding / ATP binding / 6-carboxyhexanoate--CoA ligase
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsEstrada, P. / Manandhar, M. / Dong, S.-H. / Deveryshetty, J. / Agarwal, V. / Cronan, J.E. / Nair, S.K.
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: The pimeloyl-CoA synthetase BioW defines a new fold for adenylate-forming enzymes.
Authors: Estrada, P. / Manandhar, M. / Dong, S.H. / Deveryshetty, J. / Agarwal, V. / Cronan, J.E. / Nair, S.K.
History
DepositionNov 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2May 3, 2017Group: Database references
Revision 1.3May 31, 2017Group: Database references
Revision 1.4Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 6-carboxyhexanoate--CoA ligase
B: 6-carboxyhexanoate--CoA ligase


Theoretical massNumber of molelcules
Total (without water)54,8922
Polymers54,8922
Non-polymers00
Water2,864159
1
A: 6-carboxyhexanoate--CoA ligase


Theoretical massNumber of molelcules
Total (without water)27,4461
Polymers27,4461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 6-carboxyhexanoate--CoA ligase


Theoretical massNumber of molelcules
Total (without water)27,4461
Polymers27,4461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.648, 68.211, 158.419
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 6-carboxyhexanoate--CoA ligase / Pimeloyl-CoA synthase / BioW


Mass: 27445.881 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: bioW, aq_1659 / Production host: Escherichia coli (E. coli) / References: UniProt: O67575, 6-carboxyhexanoate-CoA ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.88 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / Details: 20-30% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 7, 2015
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 22008 / % possible obs: 99.8 % / Redundancy: 6.7 % / Rsym value: 0.135 / Net I/σ(I): 11.9
Reflection shellResolution: 2.5→2.51 Å / Num. unique all: 212 / Rsym value: 0.56

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 2.5→42.018 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 23.46
RfactorNum. reflection% reflection
Rfree0.27 1125 5.12 %
Rwork0.2057 --
obs0.2089 21955 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→42.018 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3826 0 0 159 3985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083884
X-RAY DIFFRACTIONf_angle_d1.0235203
X-RAY DIFFRACTIONf_dihedral_angle_d15.6952409
X-RAY DIFFRACTIONf_chiral_restr0.054583
X-RAY DIFFRACTIONf_plane_restr0.009658
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.61380.32651540.26812549X-RAY DIFFRACTION100
2.6138-2.75160.34011280.26482563X-RAY DIFFRACTION100
2.7516-2.92390.33481540.24822526X-RAY DIFFRACTION100
2.9239-3.14960.29141460.23922593X-RAY DIFFRACTION100
3.1496-3.46640.28671230.22512572X-RAY DIFFRACTION100
3.4664-3.96770.2871480.18912612X-RAY DIFFRACTION100
3.9677-4.99760.21671310.16932640X-RAY DIFFRACTION100
4.9976-42.02430.21931410.17782775X-RAY DIFFRACTION100

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